list_ligands

Does the description disclose side effects, auth requirements, rate limits, or destructive behavior?

Annotations already declare readOnlyHint, idempotentHint, destructiveHint=false, and closed-world scope, so the safety profile is fully covered. The description adds genuinely useful context beyond that: the returned identifiers are residue names of three characters, or five for newer CCD codes — information an agent needs to build valid follow-up calls. It does not address behavior when no ligands exist or the object name is invalid.

Agents need to know what a tool does to the world before calling it. Descriptions should go beyond structured annotations to explain consequences.

Is the description appropriately sized, front-loaded, and free of redundancy?

Two short sentences, no waste. The capability statement comes first and the usage rule second, which is the correct front-loading for an agent scanning for the right tool.

Shorter descriptions cost fewer tokens and are easier for agents to parse. Every sentence should earn its place.

Given the tool's complexity, does the description cover enough for an agent to succeed on first attempt?

With one required parameter, full annotations, and an output schema, the description plus structured fields cover nearly everything needed. The only gap is edge-case behavior (empty result set, unknown object), which matters mildly because an empty list is silently ambiguous for a discovery tool.

Complex tools with many parameters or behaviors need more documentation. Simple tools need less. This dimension scales expectations accordingly.

Does the description clarify parameter syntax, constraints, interactions, or defaults beyond what the schema provides?

Only one parameter (obj_name) with 100% schema description coverage reading "Object to inspect for organic ligands." The description adds the notion of residue-name granularity but nothing further about obj_name itself, so the baseline 3 applies.

Input schemas describe structure but not intent. Descriptions should explain non-obvious parameter relationships and valid value ranges.

Does the description clearly state what the tool does and how it differs from similar tools?

States a specific verb and resource: "Lists the small-molecule (organic) ligand residue names in an object." It also scopes what is listed (organic ligands only, not waters/ions or all residues), which distinguishes it from sibling listers such as list_objects and list_chains.

Agents choose between tools based on descriptions. A clear purpose with a specific verb and resource helps agents select the right tool.

Does the description explain when to use this tool, when not to, or what alternatives exist?

Gives an explicit call-order rule: invoke this before ligand_view, pocket_view, or pharmacophore_view when the ligand residue name is unknown. The prerequisite condition is concrete and names the exact downstream alternatives, so nothing is left to inference.

Agents often have multiple tools that could apply. Explicit usage guidance like "use X instead of Y when Z" prevents misuse.